The invention provides a high-efficiency compound microbial inoculum for fermenting beds, particularly relates to a compound microbial inoculum for the fermenting beds, and a preparation method and application thereof. The compound microbial inoculum is composed of five beneficial bacterium strains (Bacillus subtilis CGMCC1.769 and CGMCC1.210, lactobacillus plantarum CICC6073, Candida tropicalis CGMCC2.587 and Trichoderma koningii CGMCC3.4290) and metabolites thereof (amylase, protease, lipase, cellulase, organic acid, bacteriophage and the like). The compound microbial inoculum is prepared by using a submerged liquid mixed fermentation technique. The method comprises the following steps: carrying out liquid submerged fermentation on the lactobacillus plantarum at 35 DEG C for 12 hours, respectively inoculating Candida tropicalis and Trichoderma koningii, carrying out mixed fermentation at 30 DEG C for 12 hours, inoculating Bacillus subtilis, carrying out liquid submerged mixed fermentation for 24 hours, respectively controlling the fermented viable count at 1-2*10<9> cfu / mL, 5-8*10<8> cfu / mL, 3-5*10<8> cfu / mL, 3-5*10<9> cfu / mL and 2-5*10<9> cfu / mL, finishing fermentation, packaging and sealing to obtain the high-efficiency compound microbial inoculum for the fermenting beds. The invention also provides application of the high-efficiency compound microbial inoculum-a preparation method of padding material. The compound microbial inoculum has the advantages of high viable count, high biological activity and low impurity bacterium pollution; the compound microbial inoculum can obviously reduce the odor of pigsties and reduce the living possibility of mosquitoes and flies, thereby achieving the ecological culture goals of no pollution and zero discharge; and the process for manufacturing the ferment bed is simple, thereby saving the padding material, human power and the like.